| line |
true |
false |
branch |
|
46
|
87 |
0 |
unless ($class =~ /Bio::Polloc::Locus::(\S+)/)
|
|
50
|
87 |
0 |
if ($type)
|
|
52
|
87 |
0 |
if $type
|
|
56
|
87 |
0 |
if ($class =~ /Bio::Polloc::Locus::(\S+)/)
|
|
58
|
87 |
0 |
if ('Bio::Polloc::RuleI'->_load_module($class)) { }
|
|
|
0 |
0 |
elsif ('Bio::Polloc::RuleI'->_load_module('Bio::Polloc::Locus::generic')) { }
|
|
64
|
87 |
0 |
if ($load)
|
|
120
|
87 |
0 |
if ($value)
|
|
122
|
0 |
87 |
unless $v
|
|
140
|
2 |
90 |
if defined $value
|
|
141
|
90 |
2 |
unless defined $$self{'_genome'}
|
|
142
|
0 |
2 |
unless UNIVERSAL::can($$self{'_genome'}, 'isa') and $$self{'_genome'}->isa('Bio::Polloc::Genome')
|
|
164
|
53 |
42 |
if defined $value
|
|
223
|
0 |
0 |
unless $_->isa('Bio::Polloc::LocusI')
|
|
263
|
0 |
3 |
if ($#args >= 0)
|
|
286
|
261 |
6 |
if ($#comments >= 0)
|
|
288
|
385 |
87 |
if defined $_
|
|
320
|
0 |
0 |
if $#_ >= 0
|
|
347
|
0 |
0 |
if $#_ >= 0
|
|
368
|
87 |
3 |
if defined $value
|
|
390
|
87 |
3 |
if defined $value
|
|
406
|
0 |
0 |
unless defined $self->from and defined $self->to
|
|
426
|
87 |
4395 |
if defined $value
|
|
473
|
121 |
39 |
if defined $value
|
|
474
|
0 |
160 |
unless (defined $$self{'_family'} or not defined $self->id)
|
|
475
|
0 |
0 |
if ($self->id =~ /(.*):\d+\.\d+/)
|
|
479
|
0 |
160 |
if not defined $$self{'_family'} and defined $self->rule
|
|
480
|
0 |
160 |
unless defined $$self{'_family'}
|
|
520
|
87 |
5 |
if defined $value
|
|
521
|
0 |
92 |
if not defined $$self{'_source'} and defined $self->rule
|
|
523
|
0 |
92 |
unless defined $$self{'_source'}
|
|
544
|
87 |
3 |
if defined $value
|
|
568
|
0 |
87 |
if (defined $value)
|
|
569
|
0 |
0 |
unless $value->isa('Bio::Polloc::RuleI')
|
|
595
|
0 |
0 |
if defined $value
|
|
622
|
0 |
87 |
if (defined $seq)
|
|
623
|
0 |
0 |
unless UNIVERSAL::can($seq, 'isa') and $seq->isa('Bio::Seq')
|
|
627
|
0 |
87 |
if (not defined $$self{'_seq'} and defined $$self{'_seq_name'} and defined $self->genome)
|
|
649
|
87 |
9 |
if defined $value
|
|
650
|
0 |
96 |
if (not defined $$self{'_seq_name'} and defined $self->seq)
|
|
671
|
0 |
0 |
if defined $self->id
|
|
712
|
0 |
0 |
unless defined $self->seq and defined $self->from and defined $self->to
|
|
716
|
0 |
0 |
if ($ref < 0) { }
|
|
|
0 |
0 |
elsif ($ref > 0) { }
|
|
717
|
0 |
0 |
if ($self->strand eq '?' or $self->strand eq '+') { }
|
|
725
|
0 |
0 |
if ($self->strand eq '?' or $self->strand eq '+') { }
|
|
733
|
0 |
0 |
if ($self->strand eq '?' or $self->strand eq '+') { }
|
|
741
|
0 |
0 |
defined $self->seq->display_id ? :
|
|
|
0 |
0 |
$revcom ? :
|
|
745
|
0 |
0 |
unless defined $seq
|
|
746
|
0 |
0 |
if $revcom
|
|
808
|
0 |
261 |
unless $value
|
|
810
|
0 |
261 |
if $value =~ /^(patt(ern)?)$/
|
|
811
|
0 |
261 |
if $value =~ /^(prof(ile)?)$/
|
|
812
|
106 |
155 |
if $value =~ /^(rep(eat)?)$/
|
|
813
|
0 |
261 |
if $value =~ /^((sequence)?sim(ilarity)?|homology|ident(ity)?)$/
|
|
814
|
0 |
261 |
if $value =~ /^(cod|cds)$/
|
|
815
|
0 |
261 |
if $value =~ /^(comp(osition)?|content)$/
|